Chromosome instability syndromes are a group of inherited conditions associated with chromosomal instability and breakage, often leading to immunodeficiency, growth retardation and increased risk of malignancy.
We performed exome sequencing on a girl with a suspected chromosome instability syndrome that manifested as growth retardation, microcephaly, developmental delay, dysmorphic features, poikiloderma, immune deficiency with pancytopenia, and myelodysplasia. She was homozygous for a previously reported splice variant, c.4444 + 3A > G in the POLE1 gene, which encodes the catalytic subunit of DNA polymerase E.
This is the second family with POLE1-deficency, with the affected individual demonstrating a more severe phenotype than previously described.
Chromosome instability syndromes are a group of inherited conditions associated with chromosomal instability and breakage which includes LIG4 [1,2], Seckel type 1 [3,4], Bloom syndrome , Nijmegen breakage syndrome [6-8], and Fanconi anemia. These genetic conditions are characterized by pre and postnatal growth retardation, microcephaly, dysmorphic features and bone marrow failure [9-11]. There are other conditions with overlapping phenotypes including microcephaly, such as Rad50 deficiency [12,13], Cernunnos-XLF syndrome  and Warsaw breakage syndrome [15-18] which can complicate molecular diagnosis. FILS syndrome (facial dysmorphism, immunodeficiency, livedo, and short stature) is a recently described condition caused by variants in POLE1, encoding the catalytic subunit of polymerase E. We describe the second family with a homozygous variant in POLE1, and a more severely affected individual, suggesting a broader phenotypic spectrum for this condition.
Patient CMH812 is a female infant born to healthy non consanguineous Palestinian parents, weighing 1745 g and measuring 38.1 cm at birth. The pregnancy was complicated by subchorionic bleeding in the first trimester, fetal abnormalities on ultrasound including intrauterine growth restriction, short long bones, suspected skull abnormalities and oligohydramnios. TORCH titers were negative. Amniocentesis revealed normal 46,XX karyotype. She was delivered at 37 weeks gestation by elective C-section secondary to breech presentation. Dysmorphic features noted included malar and mandibular hypoplasia (Figure 1A, B). Initial clinical suspicion was for primordial dwarfism such as Seckel type 1 syndrome, however her microcephaly was not as severe. Over several months, lacy reticular pigmentation was noted of the face and extremities. She had recurrent pruritic papular eruptions and skin findings progressed to include appearance of poikiloderma (Figure 1C, D). Erupted teeth were found to be small and dysplastic. She developed a feeding aversion necessitating a gastrostomy tube. Growth remained poor postnatally (Figure 2). Her motor milestones were delayed but social development was normal.
She suffered chronic rhinosinusitis and pulmonary infections with purulent otitis media. At age 20 months she was admitted to the hospital with pancytopenia, splenomegaly, hepatitis and acute CMV infection. Laboratory data showed mild bone marrow myelodysplasia, normal total B, T, and NK cells, low class switched and non switched memory B cells, and high memory T cells. She had high IgA, normal total IgG and low IgM, IgG2 and IgG4. There was no serologic response to pneumococcal vaccine (Table 1). Lymphocyte response to mitogens was normal but absent to pertussis and candida antigens . Hepatitis and pancytopenia resolved following the CMV infection. Extensive molecular and cytogenetic testing was negative, including array-CGH, telomere length studies, chromosome breakage, and gene sequencing with deletion/duplication analysis for the following genes: ATM, ATR, BLM, CENPJ, CEP152, CEP63, ERCC6, ERCC8, LIG4, LMNA, MRE11A, NBN, PCNT, RBBP8, RECQL4, SHOX, WRN, and ZMPSTE24.
Trio-exome sequencing was performed on CMH812 and her healthy parents (CMH813 & CMH814) following informed consent, and with methods as previously published [19-22]. Variants were filtered to 1% minor allele frequency, then prioritized by the American College of Medical Genetics (ACMG) categorization [23,24], OMIM identity and phenotypic assessment. This individual was homozygous for a splice-site variant, c.4444 + 3A > G, in intron 34 of the POLE1 . The parents were both heterozygous carriers (Additional file 1: Table S1). Homozygosity mapper was used to identify intervals of homozygosity and identity by descent segments (Additional file 2: Figure S1) .
The c.4444 + 3A > G variant was previously reported in consanguineous French family with three generations of affected members . FILS phenotype was variable but included macrocephaly, recurrent respiratory infections, livedo and telangiectasia, bone dysplasia, short stature, and decreased IgM and IgG. The phenotype was considered similar to that of Bloom syndrome but with normal sister chromatid exchange. Table 1 compares the clinical and cellular features of CMH812 to those of individuals with inherited chromosomal instability and breakage syndromes, as well as the first reported FILS family. Features closely matched those reported in FILS with exceptions of microcephaly and intrauterine growth restriction. Although the POLE1 variant identified in the present case is the same as previously reported, CMH812 seems to have had more significantly impaired growth and immunity, raising the hypothesis that rare variant(s) in other POLƐ subunits or MMR genes may act as phenotypic modifiers. However, no rare variant were detected in MMR genes, POLE1 interacting proteins or other DNA breakage/instability syndrome genes.
The c.4444 + 3A > G POLE1 variant confers abnormal splicing whereby exon 34 is deleted  leading to significant decrease in the POLE1 subunit . T- lymphocytes from affected individuals showed a proliferation defect as well as impaired cell cycle progression. The primary function of polymerase Ɛ1 is to synthesize DNA at the leading strand during replication [26,27], however, it is also involved in other cellular processes, including cell cycle progression and DNA repair/recombination [26,27]. Exonucleolytic proofreading and the MMR pathway act to maintain high-fidelity DNA replication and to protect against mutagenesis . Somatic and germline heterozygous missense variants in POLƐ1 have been associated with an increased cancer risk [28-32]. Functional studies in yeast showed that heterozygosity for a pathogenic allele can cause complete MMR deficiency, and that subsequent loss of heterozygosity is not required for the development of POLE-related tumors . Taken together, these findings suggest that POLE1 carriers are likely to be at increased risk for malignancy due to MMR deficiency.
In summary, we report a second family with POLE1-related disease. The clinical and immunologic features of our patient are reminiscent of LIG4 syndrome, possibly representing the more severe end of an ill-defined clinical spectrum. For this reason, POLE1 deficiency may be a more apt description of this disorder. This report illustrates the cost-effectiveness of trio-exome sequencing as a powerful diagnostic method considering that this family underwent an extensive diagnostic odyssey, with no molecular basis identified prior exome.
The project was approved by the research ethics committee of the Children’s Mercy Hospitals. Written informed consent was obtained from the patient’s legal guardians for publication of this case report. A copy of the written consent is available for review by the Editor-in-Chief of this journal.
American College of Medical Genetics
Array of comparative genomic hybridization
Facial dysmorphism immunodeficiency livedo and short stature
Intrauterine growth restriction
DNA ligase IV
DNA mismatch repair
Online Mendelian Inheritance in Man
Neonatal intensive-care unit
Polymerase chain reaction
DNA polymerase E1
Thrombocytopenia absent radii syndrome
Toxoplasmosis, other infections, rubella, cytomegalovirus (CMV), and herpes simplex virus (HSV). The “other infections” usually include syphilis, hepatitis B, coxsackie virus, Epstein-Barr virus, varicella-zoster virus, and human parvovirus
Single nucleotide polymorphism
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We are grateful to the patient and her family. We thank the other staff of the Center for Pediatric Genomic Medicine, Children’s Mercy Kansas City, and Dr. Geneviève de Saint Basile and her team for discussions. This work was supported by the Marion Merrell Dow Foundation, Children’s Mercy - Kansas City, Patton Trust, W.T. Kemper Foundation, Pat & Gil Clements Foundation, Claire Giannini Foundation, and Black & Veatch.
The accession numbers for the reference sequences are listed as follows: POLE1 NM_006231.2:,HGMD 290829429, ClinVarRCV000034317.25
1000 Genomes Project, http://www.1000genomes.org/
NHBLI Exome Sequencing Project (ESP) Exome Variant Server,
Online Mendelian Inheritance in Man (OMIM), http://www.omim.org
UCSC Genome Browser, http://genome.ucsc.edu/
The authors declare that they have no competing interests.
The authors have made the following declarations about their contributions: Conceived and designed the experiments: CJS, EF, IT, GT. Performed the experiments: CJS, EF, IT, NK, NM, LZ. Contributed reagents/materials/analysis tools: NM, EF, DZ, GT. Wrote the paper: IT, CJS, NPS, JJ. Reviewed the manuscript: DZ, EF, KC, MS, HW, NM, NR, SFK. Contributed to the recruitment and clinical investigations of the patient for the study: DZ, HW, KC, JJ, MS, NK, NPS, NS. All authors read and approved the final manuscript.
Trio-Exome sequencing data.
Homozygosity Mapping Analysis. Homozygosity mapper was used to identify intervals of homozygosity. The homozygosity scores are plotted against the physical position. Red and black bars represent the excess (red) or the shortage (black) of homozygosity (A) Eighteen loci of > 1 Mb of homozygosity were identified on seven chromosomes; loci ranged between 1.06 and 6.37 Mb in length. The length of identical by descent segments in genomes of CMH812 parents suggests that they are not closely related. However, they shared several relatively small identical segments of genome which is explained by the shared ancestry broken into pieces by the recombination events and Mendelian laws of inheritance. POLE1 lies in a 1.1 Mb region of homozygosity on chromosome 12 (chr12:132635257–133702440), which includes 20 genes (B). It is reasonable to hypothesize that the POLE1 variant, if not the result of a combination of recent origin and chance, owes its origin to a founder who lived several hundred years ago. Consistent with the rarity of the c.4444 + 3A > G variant and the small physical distances between each haplotype marker in relationship to POLE1 gene (1.1 Mb); the size of the shared haplotype may have been broken into smaller segments due to genetic drift. This assumption could explain that the same variant (c.4444 + 3A > G) has been found in two apparently unrelated FILS families.
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Thiffault, I., Saunders, C., Jenkins, J. et al. A patient with polymerase E1 deficiency (POLE1): clinical features and overlap with DNA breakage/instability syndromes. BMC Med Genet 16, 31 (2015). https://doi.org/10.1186/s12881-015-0177-y
- FILS syndrome
- Primordial dwarfism